Mercurial > repos > hepcat72 > extractsplitreads_bwamem

comparison extractSplitReads_BwaMem.xml @ 0:839c219ab0aa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
author hepcat72
date Fri, 10 Aug 2018 11:46:23 -0400
parents
children a20ac5d90c16
comparison
equal deleted inserted replaced
-1:000000000000 0:839c219ab0aa
1 <tool id="extractsplitreads_bwamem"
2 name="Extract Split Reads"
3 version="0.1.0">
4
5 <description>from bwaMEM (part of lumpy-sv)</description>
6
7 <requirements>
8 <requirement type="package" version="0.2.14a">lumpy-sv</requirement>
9 </requirements>
10
11 <!-- Not sure yet how to call the command if the lumpy-sv package in bioconda doesn't put the script in an executable location on PATH -->
12
13 <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command>
14
15 <command detect_errors="aggressive">
16 <![CDATA[
17 extractSplitReads_BwaMem
18 -i '$input'
19 -n $numSplits
20 $includeDups
21 -m $minNonOverlap
22 > '$output'
23 ]]>
24 </command>
25
26 <inputs>
27
28 <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/>
29
30 <param name="numSplits"
31 label="numSplits"
32 argument="--numSplits"
33
34 type="integer"
35 value="2"
36
37 help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." />
38
39 <param name="includeDups"
40 label="includeDups"
41 argument="--includeDups"
42
43 type="boolean"
44 truevalue="--includeDups"
45 falsevalue=""
46 checked="no"
47 value="false"
48
49 help="Include alignments marked as duplicates." />
50
51 <param name="minNonOverlap"
52 label="minNonOverlap"
53 argument="--minNonOverlap"
54
55 type="integer"
56 value="20"
57
58 help="Minimum non-overlap between split alignments on the query." />
59
60 </inputs>
61 <outputs>
62 <data format="sam" name="output" />
63 </outputs>
64
65 <tests>
66 <test>
67 <param name="input" value="JS01-BWA-MEM.splitters.sam"/>
68 <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/>
69 </test>
70 <test>
71 <param name="input" value="pe.pos_sorted.sam"/>
72 <output name="output" file="pe.pos_sorted.out.sam"/>
73 </test>
74 </tests>
75
76 <help>
77 <![CDATA[
78
79 Usage: `extractSplitReads_BwaMem -i <file>`
80
81 extractSplitReads_BwaMem v0.1.0
82
83 Author: Ira Hall
84
85 Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates.
86
87 Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405.
88
89
90 Options:
91 -h, --help show this help message and exit
92 -i FILE, --inFile=FILE
93 A SAM file or standard input (-i stdin).
94 -n INT, --numSplits=INT
95 The maximum number of split-read mappings to allow per
96 read. Reads with more are excluded. Default=2
97 -d, --includeDups Include alignments marked as duplicates. Default=False
98 -m INT, --minNonOverlap=INT
99 minimum non-overlap between split alignments on the
100 query (default=20)
101
102 ]]>
103 </help>
104
105 <citations>
106 <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation>
107 </citations>
108
109 </tool>